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Yaşar A, Ryu HJ, Esen E, Sarıoğlan İ, Deemer D, Çetin B, Yoo SH, Lindemann SR, Lee BH, Tunçil YE. The branching ratio of enzymatically synthesized α-glucans impacts microbiome and metabolic outcomes of in vitro fecal fermentation. Carbohydr Polym 2024; 335:122087. [PMID: 38616077 DOI: 10.1016/j.carbpol.2024.122087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/24/2024] [Indexed: 04/16/2024]
Abstract
The aim of this study was to evaluate the impacts of enzymatically synthesized α-glucans possessing α-1,4- and α-1,6-glucose linkages, and varying in branching ratio, on colonic microbiota composition and metabolic function. Four different α-glucans varying in branching ratio were synthesized by amylosucrase from Neisseria polysaccharea and glycogen branching enzyme from Rhodothermus obamensis. The branching ratios were found to range from 0 % to 2.8 % using GC/MS. In vitro fecal fermentation analyses (n = 8) revealed that the branching ratio dictates the short-chain fatty acid (SCFA) generation by fecal microbiota. Specifically, slightly branched (0.49 %) α-glucan resulted in generation of significantly (P < 0.05) higher amounts of propionate, compared to more-branched counterparts. In addition, the amount of butyrate generated from this α-glucan was statistically (P > 0.05) indistinguishable than those observed in resistant starches. 16S rRNA sequencing revealed that enzymatically synthesized α-glucans stimulated Lachnospiraceae and Ruminococcus related OTUs. Overall, the results demonstrated metabolic function of colonic microbiota can be manipulated by altering the branching ratio of enzymatically synthesized α-glucans, providing insights into specific structure-function relationships between dietary fibers and the colonic microbiome. Furthermore, the slightly branched α-glucans could be used as functional carbohydrates to stimulate the beneficial microbiota and SCFAs in the colon.
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Affiliation(s)
- Arife Yaşar
- Food Engineering Department, Engineering Faculty, Necmettin Erbakan University, Konya 42090, Turkiye
| | - Hye-Jung Ryu
- Department of Food Science & Biotechnology, Gachon University, Seongnam 13120, Republic of Korea
| | - Emine Esen
- Food Engineering Department, Engineering Faculty, Necmettin Erbakan University, Konya 42090, Turkiye
| | - İhsan Sarıoğlan
- Food Engineering Department, Engineering Faculty, Necmettin Erbakan University, Konya 42090, Turkiye
| | - Dane Deemer
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, 47907, IN, USA
| | - Bülent Çetin
- Food Engineering Department, Agricultural Faculty, Atatürk University, Erzurum, 25100, Turkiye
| | - Sang-Ho Yoo
- Department of Food Science & Biotechnology, Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, 47907, IN, USA; Department of Nutrition Science, Purdue University, West Lafayette 47907, IN, USA; Department of Biological Sciences, Purdue University, West Lafayette 47907, IN, USA
| | - Byung-Hoo Lee
- Department of Food Science & Biotechnology, Gachon University, Seongnam 13120, Republic of Korea
| | - Yunus E Tunçil
- Food Engineering Department, Engineering Faculty, Necmettin Erbakan University, Konya 42090, Turkiye; Medical and Cosmetic Plants Application and Research Center, Necmettin Erbakan University, Konya 42090, Turkiye.
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Abbasi E, Akçay E. Host control and species interactions jointly determine microbiome community structure. Theor Popul Biol 2024; 158:185-194. [PMID: 38925487 DOI: 10.1016/j.tpb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.
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Affiliation(s)
- Eeman Abbasi
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA
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Fricker AD, Yao T, Lindemann SR, Flores GE. Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage. FEMS Microbiol Ecol 2024; 100:fiae078. [PMID: 38794902 PMCID: PMC11180985 DOI: 10.1093/femsec/fiae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024] Open
Abstract
Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.
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Affiliation(s)
- Ashwana D Fricker
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Gilberto E Flores
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
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Zhao S, Lau R, Chen MH. Influence of chain length on the colonic fermentation of xylooligosaccharides. Carbohydr Polym 2024; 331:121869. [PMID: 38388037 DOI: 10.1016/j.carbpol.2024.121869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Xylooligosaccharides (XOS) have been employed as prebiotics containing oligomers of varying sizes or molecular ratios. XOS with a low degree of polymerization (DP) has been demonstrated to have high prebiotic potential. However, there is limited information regarding the specific chain length of XOS required to elicit distinct responses in the gut microbiota. In this study, we aimed to explore whether variations in XOS DP could alter the fate of colonic fermentation. Five XOS fractions (BWXFs) with DP ranges of >40, 20-40, 10-20, 5-10, and 2-4 were prepared by beechwood xylan autohydrolysis and tested on human gut microbiota. Extracellular XOS degradation was observed for molecules with a DP exceeding 5. BWXF treatments altered the microbial community structures, and substrate size-dependent effects on the microbial composition and metabolic outputs were observed. Bacteroidaceae were specifically enriched by xylan. Lachnospiraceae were particularly stimulated by XOS with a DP of 20-40 and 2-4. Bifidobacteriaceae were notably enriched by XOS with a DP of 5-20. High butyrate yields were obtained from cultures containing long-chain BWXFs. Microbiota responses differed with XOS DP composition changes, and microbial competition with XOS with a DP of 2-4 requires further exploration.
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Affiliation(s)
- Sainan Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Block N1.2, 62 Nanyang Drive, 637459, Singapore.
| | - Raymond Lau
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Block N1.2, 62 Nanyang Drive, 637459, Singapore.
| | - Ming-Hsu Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Block N1.2, 62 Nanyang Drive, 637459, Singapore; Institute of Food Science and Technology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
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Gurung M, Schlegel BT, Rajasundaram D, Fox R, Bode L, Yao T, Lindemann SR, LeRoith T, Read QD, Simecka C, Carroll L, Andres A, Yeruva L. Microbiota from human infants consuming secretors or non-secretors mothers' milk impacts the gut and immune system in mice. mSystems 2024; 9:e0029424. [PMID: 38530054 PMCID: PMC11019842 DOI: 10.1128/msystems.00294-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Maternal secretor status is one of the determinants of human milk oligosaccharides (HMOs) composition, which, in turn, influences the gut microbiota composition of infants. To understand if this change in gut microbiota impacts immune cell composition, intestinal morphology, and gene expression, 21-day-old germ-free C57BL/6 mice were transplanted with fecal microbiota from infants whose mothers were either secretors (SMM) or non-secretors (NSM) or from infants consuming dairy-based formula (MFM). For each group, one set of mice was supplemented with HMOs. HMO supplementation did not significantly impact the microbiota diversity; however, SMM mice had a higher abundance of genus Bacteroides, Bifidobacterium, and Blautia, whereas, in the NSM group, there was a higher abundance of Akkermansia, Enterocloster, and Klebsiella. In MFM, gut microbiota was represented mainly by Parabacteroides, Ruminococcaceae_unclassified, and Clostrodium_sensu_stricto. In mesenteric lymph node, Foxp3+ T cells and innate lymphoid cells type 2 were increased in MFM mice supplemented with HMOs, while in the spleen, they were increased in SMM + HMOs mice. Similarly, serum immunoglobulin A was also elevated in MFM + HMOs group. Distinct global gene expression of the gut was observed in each microbiota group, which was enhanced with HMOs supplementation. Overall, our data show that distinct infant gut microbiota due to maternal secretor status or consumption of dairy-based formula and HMO supplementation impacts immune cell composition, antibody response, and intestinal gene expression in a mouse model. IMPORTANCE Early life factors like neonatal diet modulate gut microbiota, which is important for the optimal gut and immune function. One such factor, human milk oligosaccharides (HMOs), the composition of which is determined by maternal secretor status, has a profound effect on infant gut microbiota. However, how the infant gut microbiota composition determined by maternal secretor status or consumption of infant formula devoid of HMOs impacts infant intestinal ammorphology, gene expression, and immune signature is not well explored. This study provides insights into the differential establishment of infant microbiota derived from infants fed by secretor or non-secretor mothers milk or those consuming infant formula and demonstrates that the secretor status of mothers promotes Bifidobacteria and Bacteroides sps. establishment. This study also shows that supplementation of pooled HMOs in mice changed immune cell composition in the spleen and mesenteric lymph nodes and immunoglobulins in circulation. Hence, this study highlights that maternal secretor status has a role in infant gut microbiota composition, and this, in turn, can impact host gut and immune system.
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Affiliation(s)
- Manoj Gurung
- Microbiome and Metabolism Research Unit (MMRU), USDA-ARS, SEA, Arkansas Children’s Nutrition Center, Little Rock, Arkansas, USA
| | - Brent Thomas Schlegel
- University of Pittsburgh Medical Center (UPMC), Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dhivyaa Rajasundaram
- University of Pittsburgh Medical Center (UPMC), Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Renee Fox
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Lars Bode
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tianming Yao
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana, USA
| | - Stephen R. Lindemann
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana, USA
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Christy Simecka
- Division of Laboratory Animal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laura Carroll
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aline Andres
- Microbiome and Metabolism Research Unit (MMRU), USDA-ARS, SEA, Arkansas Children’s Nutrition Center, Little Rock, Arkansas, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laxmi Yeruva
- Microbiome and Metabolism Research Unit (MMRU), USDA-ARS, SEA, Arkansas Children’s Nutrition Center, Little Rock, Arkansas, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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Carnicero-Mayo Y, Sáenz de Miera LE, Ferrero MÁ, Navasa N, Casqueiro J. Modeling Dynamics of Human Gut Microbiota Derived from Gluten Metabolism: Obtention, Maintenance and Characterization of Complex Microbial Communities. Int J Mol Sci 2024; 25:4013. [PMID: 38612823 PMCID: PMC11012253 DOI: 10.3390/ijms25074013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Western diets are rich in gluten-containing products, which are frequently poorly digested. The human large intestine harbors microorganisms able to metabolize undigested gluten fragments that have escaped digestion by human enzymatic activities. The aim of this work was obtaining and culturing complex human gut microbial communities derived from gluten metabolism to model the dynamics of healthy human large intestine microbiota associated with different gluten forms. For this purpose, stool samples from six healthy volunteers were inoculated in media containing predigested gluten or predigested gluten plus non-digested gluten. Passages were carried out every 24 h for 15 days in the same medium and community composition along time was studied via V3-V4 16S rDNA sequencing. Diverse microbial communities were successfully obtained. Moreover, communities were shown to be maintained in culture with stable composition for 14 days. Under non-digested gluten presence, communities were enriched in members of Bacillota, such as Lachnospiraceae, Clostridiaceae, Streptococcaceae, Peptoniphilaceae, Selenomonadaceae or Erysipelotrichaceae, and members of Actinomycetota, such as Bifidobacteriaceae and Eggerthellaceae. Contrarily, communities exposed to digested gluten were enriched in Pseudomonadota. Hence, this study shows a method for culture and stable maintenance of gut communities derived from gluten metabolism. This method enables the analysis of microbial metabolism of gluten in the gut from a community perspective.
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Affiliation(s)
- Yaiza Carnicero-Mayo
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
| | - Luis E. Sáenz de Miera
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
| | - Miguel Ángel Ferrero
- Área de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de León, 24007 León, Spain; (M.Á.F.); (N.N.)
| | - Nicolás Navasa
- Área de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de León, 24007 León, Spain; (M.Á.F.); (N.N.)
| | - Javier Casqueiro
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
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Xu Y, Liu X, Ma M, Wang M, Hua W, Yao T, Sui Z. Structural and rheological characterization of water-soluble and alkaline-soluble fibers from hulless barley. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:2897-2906. [PMID: 38018273 DOI: 10.1002/jsfa.13182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Highland hulless barley has garnered attention as a promising economic product and a potential healthy food ingredient. The present study aimed to comprehensively investigate the molecular structure of extractable fibers obtained from a specific highland hulless barley. Water-soluble fiber (WSF) and alkaline-soluble fiber (ASF) were extracted using enzymatic digestion and an alkaline method, respectively. The purified fibers underwent a thorough investigation for their structural characterization. RESULTS The monosaccharide composition revealed that WSF primarily consisted of glucose (91.7%), whereas ASF was composed of arabinose (54.5%) and xylose (45.5%), indicating the presence of an arabinoxylan molecule with an A/X ratio of 1.2. The refined structural information was further confirmed through methylation, 1 H NMR and Fourier-transform infrared spectroscopy analyses. WSF fiber exclusively exhibited α-anomeric patterns, suggesting it was an α-glucan. It has a low molecular weight of 5 kDa, as determined by gel permeation chromatography. Conversely, ASF was identified as a heavily branched arabinoxylan with 41.55% of '→2,3,4)-Xylp-(1→' linkages. ASF and WSF exhibited notable differences in their morphology, water absorption capabilities and rheological properties. CONCLUSION Based on these findings, molecular models of WSF and ASF were proposed. The deep characterization of these fiber structures provides valuable insights into their physicochemical and functional properties, thereby unlocking their potential applications in the food industry. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yuting Xu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoning Liu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Mengting Ma
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingming Wang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Weifeng Hua
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Zhongquan Sui
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Zhang Y, Ye Y, Guo J, Wang M, Li X, Ren Y, Zhu W, Yu K. Effects of 2'-fucosyllactose on the composition and metabolic activity of intestinal microbiota from piglets after in vitro fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1553-1563. [PMID: 37815100 DOI: 10.1002/jsfa.13037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND As indigestible carbohydrates, milk oligosaccharides possess various benefits for newborns, mainly through intestinal microbiota, among which 2'-fucosyllactose (2'-FL) is the most predominant milk oligosaccharide. However, knowledge about the fermentative characteristics of 2'-FL in the gut remains limited, especially in the small intestine. The aim of this study is to explore the differential fermentability of 2'-FL by the small and large intestinal microbiota of piglets using fructo-oligosaccharide (FOS) and lactose as controls in an in vitro batch fermentation experiment. During fermentation, microbial composition was characterized along with gas production and short-chain fatty acid production. RESULTS 2'-Fucosyllactose showed differential fermentability in jejunal and colonic fermentation. Compared with the colon, 2'-FL produced less gas in the jejunum than in the FOS and lactose groups (P < 0.05). Meanwhile, 2'-FL exhibited a different influence on the microbial composition and metabolism in the jejunum and colon compared with FOS and lactose. In the jejunum, compared with the FOS and lactose groups, the 2'-FL group showed a higher abundance of Bacteroides, Prevotella, and Blautia, but a lower abundance of Streptococcus and Lactobacillus (P < 0.05), with a higher level of propionate and a lower level of lactate during fermentation (P < 0.05). In the colon, compared with the FOS and lactose groups, 2'-FL increased the abundance of Blautia, Faecalibacterium, and Lachnospiraceae FCS020, but decreased the abundance of Prevotella_9, Succinivibrio, and Megasphaera (P < 0.05) with an increase in acetate production (P < 0.05). CONCLUSION Overall, the results suggested that the small intestinal microbiota had the potential to ferment milk oligosaccharides. Meanwhile, in comparison with FOS and lactose, 2'-FL selectively stimulated the growth of propionate-producing bacteria in the jejunum and acetate-producing bacteria in the colon. These results demonstrated the differences in fermentation properties of 2'-FL by small and large intestinal microbiota and provided new evidence for the application of 2'-FL in optimizing gut microbiota. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yanan Zhang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yanxin Ye
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Jiaqing Guo
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Mengting Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Xuan Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yuting Ren
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Kaifan Yu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
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Zhao S, Lau R, Zhong Y, Chen MH. Lactate cross-feeding between Bifidobacterium species and Megasphaera indica contributes to butyrate formation in the human colonic environment. Appl Environ Microbiol 2024; 90:e0101923. [PMID: 38126785 PMCID: PMC10807433 DOI: 10.1128/aem.01019-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Butyrate, a physiologically active molecule, can be synthesized through metabolic interactions among colonic microorganisms. Previously, in a fermenting trial of human fecal microbiota, we observed that the butyrogenic effect positively correlated with the increasing Bifidobacterium population and an unidentified Megasphaera species. Therefore, we hypothesized that a cross-feeding phenomenon exists between Bifidobacterium and Megasphaera, where Megasphaera is the butyrate producer, and its growth relies on the metabolites generated by Bifidobacterium. To validate this hypothesis, three bacterial species (B. longum, B. pseudocatenulatum, and M. indica) were isolated from fecal cultures fermenting hydrolyzed xylan; pairwise cocultures were conducted between the Bifidobacterium and M. indica isolates; the microbial interactions were determined based on bacterial genome information, cell growth, substrate consumption, metabolite quantification, and metatranscriptomics. The results indicated that two Bifidobacterium isolates contained distinct gene clusters for xylan utilization and expressed varying substrate preferences. In contrast, M. indica alone scarcely grew on the xylose-based substrates. The growth of M. indica was significantly elevated by coculturing it with bifidobacteria, while the two Bifidobacterium species responded differently in the kinetics of cell growth and substrate consumption. Coculturing led to the depletion of lactate and increased the formation of butyrate. An RNA-seq analysis further revealed the upregulation of M. indica genes involved in the lactate utilization and butyrate formation pathways. We concluded that lactate generated by Bifidobacterium through catabolizing xylose fueled the growth of M. indica and triggered the synthesis of butyrate. Our findings demonstrated a novel cross-feeding mechanism to generate butyrate in the human colon.IMPORTANCEButyrate is an important short-chain fatty acid that is produced in the human colon through microbial fermentation. Although many butyrate-producing bacteria exhibit a limited capacity to degrade nondigestible food materials, butyrate can be formed through cross-feeding microbial metabolites, such as acetate or lactate. Previously, the literature has explicated the butyrate-forming links between Bifidobacterium and Faecalibacterium prausnitzii and between Bifidobacterium and Eubacterium rectale. In this study, we provided an alternative butyrate synthetic pathway through the interaction between Bifidobacterium and Megasphaera indica. M. indica is a species named in 2014 and is indigenous to the human intestinal tract. Scientific studies explaining the function of M. indica in the human colon are still limited. Our results show that M. indica proliferated based on the lactate generated by bifidobacteria and produced butyrate as its end metabolic product. The pathways identified here may contribute to understanding butyrate formation in the gut microbiota.
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Affiliation(s)
- Sainan Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Raymond Lau
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yang Zhong
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Ming-Hsu Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
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10
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McNichol SM, Sanchez-Quete F, Loeb SK, Teske AP, Shah Walter SR, Mahmoudi N. Dynamics of carbon substrate competition among heterotrophic microorganisms. THE ISME JOURNAL 2024; 18:wrae018. [PMID: 38366177 PMCID: PMC10942773 DOI: 10.1093/ismejo/wrae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/06/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These interactions are dynamic and shaped by the composition and availability of resources in their surrounding environment. Heterotrophic microorganisms inhabiting marine environments often encounter fluctuations in the quality and quantity of carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how the chemical complexity of carbon substrates affects competition and growth dynamics between two heterotrophic marine isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays and measured rates of microbial CO2 production along with associated isotopic signatures (13C and 14C) to quantify the impact of these interactions on organic matter remineralization. The observed cell densities revealed substrate-driven interactions: one species exhibited a competitive advantage and quickly outgrew the other when incubated with a labile compound whereas both species seemed to coexist harmoniously in the presence of more complex organic matter. Rates of CO2 respiration revealed that coincubation of these isolates enhanced organic matter turnover, sometimes by nearly 2-fold, compared to their incubation as mono-cultures. Isotopic signatures of respired CO2 indicated that coincubation resulted in a greater remineralization of macromolecular organic matter. These results demonstrate that simple substrates promote competition whereas high substrate complexity reduces competitiveness and promotes the partitioning of degradative activities into distinct niches, facilitating coordinated utilization of the carbon pool. Taken together, this study yields new insight into how the quality of organic matter plays a pivotal role in determining microbial interactions within marine environments.
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Affiliation(s)
- Samuel M McNichol
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
| | - Fernando Sanchez-Quete
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Stephanie K Loeb
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd, Lewes, DE 19958, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
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11
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Xu H, Pudlo NA, Cantu-Jungles TM, Tuncil YE, Nie X, Kaur A, Reuhs BL, Martens EC, Hamaker BR. When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures. ISME COMMUNICATIONS 2024; 4:ycae037. [PMID: 38645272 PMCID: PMC11032216 DOI: 10.1093/ismeco/ycae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 04/23/2024]
Abstract
Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 (Bacteroides cellulosilyticus) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures. In a competition experiment, B. cellulosilyticus growth was favored over B. ovatus on the complex AX-based structure. On the other hand, on the simple structure, B. ovatus strongly outcompeted B. cellulosilyticus, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.
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Affiliation(s)
- Haidi Xu
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
- Present address: Nestlé Health Science, Shanghai, P.R. China
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, Medical Sciences Research Building II, 1150 W Medical Center Dr., University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Thaisa M Cantu-Jungles
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Yunus E Tuncil
- Food Engineering Department, Yeni Meram Boulevard Kasım Halife Street, Necmettin Erbakan University, Konya 42090, Turkey
| | - Xin Nie
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Amandeep Kaur
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Bradley L Reuhs
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Eric C Martens
- Department of Microbiology and Immunology, Medical Sciences Research Building II, 1150 W Medical Center Dr., University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
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12
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Yao T, Deemer DG, Chen MH, Reuhs BL, Hamaker BR, Lindemann SR. Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota. Carbohydr Polym 2023; 316:121039. [PMID: 37321733 DOI: 10.1016/j.carbpol.2023.121039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/27/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023]
Abstract
Dietary fibers are known to modulate microbiome composition, but it is unclear to what extent minor fiber structural differences impact community assembly, microbial division of labor, and organismal metabolic responses. To test the hypothesis that fine linkage variations afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fecal fermentation with four fecal inocula and measured responses using an integrated multi-omics approach. Two sorghum arabinoxylans (SAXs) were fermented, with one (RSAX) having slightly more complex branch linkages than the other (WSAX). Although there were minor glycoysl linkage differences, consortia on RSAX retained much higher species diversity (42 members) than on WSAX (18-23 members) with distinct species-level genomes and metabolic outcomes (e.g., higher short chain fatty acid production from RSAX and more lactic acid produced from WSAX). The major SAX-selected members were from genera of Bacteroides and Bifidobacterium and family Lachnospiraceae. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials among key members; however, CAZyme genes enriched in different consortia displayed various catabolic domain fusions with diverse accessory motifs that differ among the two SAX types. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia.
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Affiliation(s)
- Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Dane G Deemer
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Ming-Hsu Chen
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA; Institute of Food Science and Technology of National Taiwan University. No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Bradley L Reuhs
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
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13
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Farooq A, Lee M, Han S, Jung GY, Kim SJ, Jung MY. Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces. Microbiol Spectr 2023; 11:e0504822. [PMID: 37707449 PMCID: PMC10581053 DOI: 10.1128/spectrum.05048-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/31/2023] [Indexed: 09/15/2023] Open
Abstract
Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.
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Affiliation(s)
- Adeel Farooq
- Research Institute for Basic Sciences (RIBS), Jeju National University, Jeju, South Korea
| | - Myunglip Lee
- Department of Marine Life Science, Jeju National University, Jeju, South Korea
| | - Saem Han
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Gi-Yong Jung
- Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, South Korea
| | - So-Jeong Kim
- Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
- Department of Science Education, Jeju National University, Jeju, South Korea
- Jeju Microbiome Center, Jeju National University, Jeju, South Korea
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14
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Ho E, Drake VJ, Michels AJ, Nkrumah-Elie YM, Brown LL, Scott JM, Newman JW, Shukitt-Hale B, Soumyanath A, Chilton FH, Lindemann SR, Shao A, Mitmesser SH. Perspective: Council for Responsible Nutrition Science in Session. Optimizing Health with Nutrition-Opportunities, Gaps, and the Future. Adv Nutr 2023; 14:948-958. [PMID: 37270030 PMCID: PMC10509435 DOI: 10.1016/j.advnut.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/20/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023] Open
Abstract
Achieving optimal health is an aspirational goal for the population, yet the definition of health remains unclear. The role of nutrition in health has evolved beyond correcting malnutrition and specific deficiencies and has begun to focus more on achieving and maintaining 'optimal' health through nutrition. As such, the Council for Responsible Nutrition held its October 2022 Science in Session conference to advance this concept. Here, we summarize and discuss the findings of their Optimizing Health through Nutrition - Opportunities and Challenges workshop, including several gaps that need to be addressed to advance progress in the field. Defining and evaluating various indices of optimal health will require overcoming these key gaps. For example, there is a strong need to develop better biomarkers of nutrient status, including more accurate markers of food intake, as well as biomarkers of optimal health that account for maintaining resilience-the ability to recover from or respond to stressors without loss to physical and cognitive performance. In addition, there is a need to identify factors that drive individualized responses to nutrition, including genotype, metabotypes, and the gut microbiome, and to realize the opportunity of precision nutrition for optimal health. This review outlines hallmarks of resilience, provides current examples of nutritional factors to optimize cognitive and performance resilience, and gives an overview of various genetic, metabolic, and microbiome determinants of individualized responses.
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Affiliation(s)
- Emily Ho
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon; Nutrition Program, College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon.
| | - Victoria J Drake
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon
| | | | | | - LaVerne L Brown
- National Institutes of Health, Office of Dietary Supplements, Bethesda, Maryland
| | - Jonathan M Scott
- Consortium for Health and Military Performance, Department of Military and Emergency Medicine, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, Maryland
| | - John W Newman
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, California
| | - Barbara Shukitt-Hale
- United States Department of Agriculture, Agricultural Research Service, Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts
| | - Amala Soumyanath
- BENFRA Botanical Dietary Supplements Research Center, Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - Floyd H Chilton
- Center for Precision Nutrition and Wellness, University of Arizona, Tucson, Arizona; School of Nutritional Sciences and Wellness, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, Indiana
| | - Andrew Shao
- ChromaDex External Research Program, Los Angeles, California
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15
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McChalicher CW, Auniņš JG. Drugging the microbiome and bacterial live biotherapeutic consortium production. Curr Opin Biotechnol 2022; 78:102801. [PMID: 36228531 DOI: 10.1016/j.copbio.2022.102801] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 12/14/2022]
Abstract
Research leading to characterization, quantification, and functional attribution of the microbes throughout the human body has led to many drug-development programs. These programs aim to manipulate a patient's microbiome through the addition of new strains or functions, the subtraction of deleterious microbes, or the rebalancing of the existing population through various drug modalities. Here, we present a general overview of those modalities with a specific focus on bacterial live biotherapeutic products (LBPs). The bacterial LBP modality has unique concerns to ensure product quality, thus, topics related to manufacturing, quality control, and regulation are addressed.
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Affiliation(s)
| | - John G Auniņš
- Seres Therapeutics Inc, 200 Sidney St, Cambridge, MA 02139, United States.
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16
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Couture G, Luthria DL, Chen Y, Bacalzo NP, Tareq FS, Harnly J, Phillips KM, Pehrsson PR, McKillop K, Fukagawa NK, Lebrilla CB. Multi-Glycomic Characterization of Fiber from AOAC Methods Defines the Carbohydrate Structures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14559-14570. [PMID: 36382383 DOI: 10.1021/acs.jafc.2c06191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dietary fiber has long been known to be an essential component of a healthy diet, and recent investigations into the gut microbiome-health paradigm have identified fiber as a prime determinant in this interaction. Further, fiber is now known to impact the gut microbiome in a structure-specific manner, conferring differential bioactivities to these specific structures. However, current analytical methods for food carbohydrate analysis do not capture this important structural information. To address this need, we utilized rapid-throughput LC-MS methods to develop a novel analytical pipeline to determine the structural composition of soluble and insoluble fiber fractions from two AOAC methods (991.43 and 2017.16) at the total monosaccharide, glycosidic linkage, and free saccharide level. Two foods were chosen for this proof-of-concept study: oats and potato starch. For oats, both AOAC methods gave similar results. Insoluble fiber was found to be comprised of linkages corresponding to β-glucan, arabinoxylan, xyloglucan, and mannan, while soluble fiber was found to be mostly β-glucan, with small amounts of arabinogalactan. For raw potato starch, each AOAC method gave markedly different results in the soluble fiber fractions. These observed differences are attributable to the resistant starch content of potato starch and the different starch digestion conditions used in each method. Together, these tools are a means to obtain the complex structures present within dietary fiber while retaining "classical" determinations such as soluble and insoluble fiber. These efforts will provide an analytical framework to connect gravimetric fiber determinations with their constituent structures to better inform gut microbiome and clinical nutrition studies.
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Affiliation(s)
- Garret Couture
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
| | - Devanand L Luthria
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Ye Chen
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
| | - Nikita P Bacalzo
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
| | - Fakir S Tareq
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - James Harnly
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Katherine M Phillips
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Pamela R Pehrsson
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Kyle McKillop
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Naomi K Fukagawa
- USDA Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland 20705, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California Davis, Davis, California 95616, United States
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17
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Du G, Sun Z, Bao S, Zhong Q, Yang S. Diversity of bacterial community in Jerusalem artichoke (Helianthus tuberosus L.) during storage is associated with the genotype and carbohydrates. Front Microbiol 2022; 13:986659. [PMID: 36187957 PMCID: PMC9520535 DOI: 10.3389/fmicb.2022.986659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Jerusalem artichoke (JA) is a fructan-accumulating crop that has gained popularity in recent years. The objective of the present study was to determine the dynamics of the JA-microbiome during storage. The microbial population on the surface of the JA tuber was determined by next-generation sequencing of 16S rRNA amplicons. Subsequently, the changes in carbohydrate and degree of polymerization of fructan in tubers during storage were measured. Among different genotypes of JA varieties, intergeneric differences were observed in the diversity and abundance of bacterial communities distributed on the surface of tubers. Additionally, bacterial diversity was significantly higher in storage-tolerant varieties relative to the storage-intolerant varieties. Redundancy analysis (RDA) and the correlation matrix indicated a relationship between changes in the carbohydrates and microbial community succession during tuber storage. The tuber decay rate correlated positively with the degree of polymerization of fructan. Moreover, Dysgonomonas and Acinetobacter in perishable varieties correlated significantly with the decay rate. Therefore, the bacteria associated with the decay rate may be involved in the degradation of the degree of polymerization of fructan. Furthermore, Serratia showed a significant positive correlation with inulin during storage but a negative correlation with the decay rate, suggesting its antagonistic role against pathogenic bacteria on the surface of JA tubers. However, the above correlation was not observed in the storage-tolerant varieties. Functional annotation analysis revealed that storage-tolerant JA varieties maintain tuber quality through enrichment of biocontrol bacteria, including Flavobacterium, Sphingobacterium, and Staphylococcus to resist pathogens. These results suggested that crop genotype and the structural composition of carbohydrates may result in differential selective enrichment effects of microbial communities on the surface of JA varieties. In this study, the relationship between microbial community succession and changes in tuber carbohydrates during JA storage was revealed for the first time through the combination of high-throughput sequencing, high-performance liquid chromatography (HPLC), and high-performance ion-exchange chromatography (HPIC). Overall, the findings of this study are expected to provide new insights into the dynamics of microbial-crop interactions during storage.
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Affiliation(s)
- Guolian Du
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Zhu Sun
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Shanhua Bao
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Qiwen Zhong
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Qinghai University, Xining, China
- *Correspondence: Qiwen Zhong,
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
- Shipeng Yang,
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18
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Zhang Y, Zhao Y, Yang W, Song G, Zhong P, Ren Y, Zhong G. Structural complexity of Konjac glucomannan and its derivatives governs the diversity and outputs of gut microbiota. Carbohydr Polym 2022; 292:119639. [DOI: 10.1016/j.carbpol.2022.119639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/02/2022]
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19
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Frolova MS, Suvorova IA, Iablokov SN, Petrov SN, Rodionov DA. Genomic reconstruction of short-chain fatty acid production by the human gut microbiota. Front Mol Biosci 2022; 9:949563. [PMID: 36032669 PMCID: PMC9403272 DOI: 10.3389/fmolb.2022.949563] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
Short-chain fatty acids (SCFAs) including acetate, formate, propionate, and butyrate are the end products of dietary fiber and host glycan fermentation by the human gut microbiota (HGM). SCFAs produced in the column are of utmost importance for host physiology and health. Butyrate and propionate improve gut health and play a key role in the neuroendocrine and immune systems. Prediction of HGM metabolic potential is important for understanding the influence of diet and HGM-produced metabolites on human health. We conducted a detailed metabolic reconstruction of pathways for the synthesis of SCFAs and L- and D-lactate, as additional fermentation products, in a reference set of 2,856 bacterial genomes representing strains of >800 known HGM species. The reconstructed butyrate and propionate pathways included four and three pathway variants, respectively, that start from different metabolic precursors. Altogether, we identified 48 metabolic enzymes, including five alternative enzymes in propionate pathways, and propagated their occurrences across all studied genomes. We established genomic signatures for reconstructed pathways and classified genomes according to their simplified binary phenotypes encoding the ability (“1”) or inability (“0”) of a given organism to produce SCFAs. The resulting binary phenotypes combined into a binary phenotype matrix were used to assess the SCFA synthesis potential of HGM samples from several public metagenomic studies. We report baseline and variance for Community Phenotype Indices calculated for SCFAs production capabilities in 16S metagenomic samples of intestinal microbiota from two large national cohorts (American Gut Project, UK twins), the Hadza hunter-gatherers, and the young children cohort of infants with high-risk for type 1 diabetes. We further linked the predicted SCFA metabolic capabilities with available SCFA concentrations both for in vivo fecal samples and in vitro fermentation samples from previous studies. Finally, we analyzed differential representation of individual SCFA pathway genes across several WGS metagenomic datasets. The obtained collection of SCFA pathway genes and phenotypes enables the predictive metabolic phenotype profiling of HGM datasets and enhances the in silico methodology to study cross-feeding interactions in the gut microbiomes.
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Affiliation(s)
- Maria S. Frolova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Inna A. Suvorova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Stanislav N. Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Sergei N. Petrov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- *Correspondence: Dmitry A. Rodionov,
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20
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Romero Marcia AD, Yao T, Chen MH, Oles RE, Lindemann SR. Fine Carbohydrate Structure of Dietary Resistant Glucans Governs the Structure and Function of Human Gut Microbiota. Nutrients 2021; 13:nu13092924. [PMID: 34578800 PMCID: PMC8467459 DOI: 10.3390/nu13092924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 01/01/2023] Open
Abstract
Increased dietary fiber consumption has been shown to increase human gut microbial diversity, but the mechanisms driving this effect remain unclear. One possible explanation is that microbes are able to divide metabolic labor in consumption of complex carbohydrates, which are composed of diverse glycosidic linkages that require specific cognate enzymes for degradation. However, as naturally derived fibers vary in both sugar composition and linkage structure, it is challenging to separate out the impact of each of these variables. We hypothesized that fine differences in carbohydrate linkage structure would govern microbial community structure and function independently of variation in glycosyl residue composition. To test this hypothesis, we fermented commercially available soluble resistant glucans, which are uniformly composed of glucose linked in different structural arrangements, in vitro with fecal inocula from each of three individuals. We measured metabolic outputs (pH, gas, and short-chain fatty acid production) and community structure via 16S rRNA amplicon sequencing. We determined that community metabolic outputs from identical glucans were highly individual, emerging from divergent initial microbiome structures. However, specific operational taxonomic units (OTUs) responded similarly in growth responses across individuals’ microbiota, though in context-dependent ways; these data suggested that certain taxa were more efficient in competing for some structures than others. Together, these data support the hypothesis that variation in linkage structure, independent of sugar composition, governs compositional and functional responses of microbiota.
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Affiliation(s)
- Arianna D. Romero Marcia
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Ming-Hsu Chen
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Renee E. Oles
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Stephen R. Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-765-494-9207
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21
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Zhao S, Dien BS, Lindemann SR, Chen MH. Controlling autohydrolysis conditions to produce xylan-derived fibers that modulate gut microbiota responses and metabolic outputs. Carbohydr Polym 2021; 271:118418. [PMID: 34364559 DOI: 10.1016/j.carbpol.2021.118418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 11/24/2022]
Abstract
Autohydrolysis is used for producing xylan-derived oligosaccharides from lignocellulosic biomass. Although numerous studies report optimized autohydrolysis conditions for various plants, few of these studies correlate process parameters with the resulting structural properties to their impact on intestinal bacterial communities. Thus, to further clarify these relationships, beechwood xylan (BWX)-derived substrates, processed under five conditions, were fermented in vitro by human gut microbiota. Autohydrolysis reduced the mean molecular size and substitutions of BWX. Distinct fermentation kinetics were observed with differing processing of BWX substrates, which correlated with impacts on community species evenness. The relative abundances of Bacteroides, Fusicatenibacter, Bifidobacterium, and Megasphaera within the fermentations varied with processing conditions. While the total short-chain fatty acid concentrations were the same among the treatments, processing conditions varied the extent of propionate and butyrate generation. Autolysis parameters may be an important tool for optimizing beneficial effects of xylan-derived fibers on human gut microbiota structure and function.
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Affiliation(s)
- Sainan Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Block N1.2, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Bruce S Dien
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States; Department of Nutrition Science, Purdue University, 700 W. State Street, West Lafayette, IN 47907, United States
| | - Ming-Hsu Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Block N1.2, 62 Nanyang Drive, Singapore 637459, Singapore.
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22
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Nadalin S, Jakovac H, Peitl V, Karlović D, Buretić-Tomljanović A. Dysregulated inflammation may predispose patients with serious mental illnesses to severe COVID‑19 (Review). Mol Med Rep 2021; 24:611. [PMID: 34184073 PMCID: PMC8258463 DOI: 10.3892/mmr.2021.12250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Genetic and nongenetic factors associated with an increased inflammatory response may mediate a link between severe coronavirus disease 2019 (COVID‑19) and serious mental illness (SMI). However, systematic assessment of inflammatory response‑related factors associated with SMI that could influence COVID‑19 outcomes is lacking. In the present review, dietary patterns, smoking and the use of psychotropic medications are discussed as potential extrinsic risk factors and angiotensin‑converting enzyme (ACE) insertion/deletion (I/D) gene polymorphisms are considered as potential intrinsic risk factors. A genetics‑based prediction model for SMI using ACE‑I/D genotyping is also proposed for use in patients experiencing severe COVID‑19. Furthermore, the literature suggests that ACE inhibitors may have protective effects against SMI or severe COVID‑19, which is often linked to hypertension and other cardiovascular comorbidities. For this reason, we hypothesize that using these medications to treat patients with severe COVID‑19 might yield improved outcomes, including in the context of SMI associated with COVID‑19.
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Affiliation(s)
- Sergej Nadalin
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Hrvoje Jakovac
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Vjekoslav Peitl
- Department of Psychiatry, Sestre Milosrdnice University Hospital Center and Catholic University of Croatia, 10000 Zagreb, Croatia
| | - Dalibor Karlović
- Department of Psychiatry, Sestre Milosrdnice University Hospital Center and Catholic University of Croatia, 10000 Zagreb, Croatia
| | - Alena Buretić-Tomljanović
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
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23
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Lindemann SR. A piece of the pie: engineering microbiomes by exploiting division of labor in complex polysaccharide consumption. Curr Opin Chem Eng 2020; 30:96-102. [PMID: 32968619 DOI: 10.1016/j.coche.2020.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Although microbes competing for simple substrates are well-known to obey the ecological competitive exclusion principle, little is known regarding how complex substrates influence the ecology of microbial communities. The vast structural diversity of polysaccharides makes them ideal substrates for cooperative microbial degradation. Potential mechanisms for division of metabolic labor in microbial communities consuming polysaccharides are 1) complementary differences in gene content, 2) alternate regulation of polysaccharide degradation genes, 3) subtle differences in hydrolytic enzyme functionality, and 4) specialization in transport and consumption of hydrolysis products. Engineering division of labor in polysaccharide degradation using these mechanisms as control points may improve our ability to engineer microbiomes for improved productivity and stability in diverse environments.
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Affiliation(s)
- Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907 USA.,Department of Nutrition Science, Purdue University, West Lafayette, IN 47907 USA
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